In 1964, three civil rights workers — two Jewish and one black — go missing while in Jessup County, Mississippi, organizing a voter registry for African Americans. The FBI sends two agents, Alan Ward and Rupert Anderson, a former Mississippi sheriff, to investigate. Ward is a Northerner, senior in rank but younger than Anderson, and approaches the investigation by the book, whereas Anderson is more nuanced in his approach. The pair find it difficult to conduct interviews with the local townspeople, as Sheriff Ray Stuckey and his deputies exert influence over the public, and are linked to a branch of the Ku Klux Klan. The wife of Deputy Sheriff Clinton Pell reveals to Anderson in a discreet conversation that the three missing men have been murdered. Their bodies are later found buried in an earthen dam. Stuckey deduces Mrs. Pell’s confession to the FBI and informs Pell, who brutally beats his wife in retribution.
This is a turning point in the plot. Ward and Anderson’s different approaches spill over into a physical fight between the two; Ward wins but concedes his methods have been ineffective and he gives Anderson carte blanche to deal with the problem. Anderson devises a plan to indict members of the Klan for the murders. The FBI arranges a kidnapping of Mayor Tilman, taking him to a remote shack. There, he is left with a black man, who threatens to castrate him unless he speaks out. Tilman gives him a full description of the killings, including the names of those involved. The abductor is revealed to be an FBI operative assigned to intimidate Tilman. Although his statement is not admissible in court due to coercion, Tilman’s information proves valuable to the investigators. Anderson beats Pell up inside a barbershop after cutting him with a shaving blade.
Anderson and Ward exploit the new information to concoct a plan, luring identified Klan collaborators to a bogus meeting. The Klan members soon realize that they have been set up, and leave without discussing the murders. The FBI then concentrate on Lester Cowens, a Klansman of interest who exhibits a nervous demeanor, which the agents believe might yield a confession. The FBI pick him up and interrogate him. Later, Cowens is at home when his window is shattered by a shotgun blast. After seeing a burning cross on his lawn, he attempts to flee in his truck, but is caught by several hooded men who intend to hang him. The FBI arrive to rescue him, having staged the whole scenario; the hooded men are revealed to be other agents.
Cowens, believing that his fellow Klansmen have threatened his life because of his admissions to the FBI, incriminates his accomplices. The Klansmen are all charged with civil rights violations, as this can be prosecuted at the federal level. Most of the perpetrators are found guilty and receive sentences from three to ten years in prison, with the exception of Stuckey, who is acquitted of all charges. Tilman is later found dead by the FBI in an apparent suicide. Mrs. Pell returns to her home, which has been completely ransacked by vandals, and resolves to stay and rebuild her life, free of her husband. Before leaving town, Anderson and Ward visit an integrated congregation, gathered at an African-American cemetery, where the black civil rights activist’s desecrated gravestone reads, “Not Forgotten”.